I am having some trouble with an installed debian on a machine. While I have all data backed up, the configuration of installed packages is also critical to me. Does anybody know a way to either re-install the OS while keeping ideally all of /etc and /home or alternatively at least get a fresh debian install will all previously installed packages which I would only have to reconfigure plus copy my data

Keep backups

Essentially, the problem is to avoid that period of occasional annoyance after reinstalling when you run into packages you haven't reinstalled. (Build dependencies can be a pain, since you don't always remember the package name, or even what they all were!)
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JefromiJun 18 '11 at 13:41

Well, I used to have the same annoyance. But recently I have grown accustomed to just starting from scratch, installing a few essentials from the top of my mind and for the reset ubuntu will automatically suggest which 'apt-get install' command will install a missing program in bash. Don't know whether that is Ubuntu-specific, but it sure rocks. It's always a matter of seconds, no slowdown at all (I must add, that I do have skipped a minor ubuntu-release in the recent past)
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seheJun 18 '11 at 14:21

Yeah, it's usually not too bad. But sometimes it's trickier - say you're trying to build something like mpd from scratch, and you know it needs some libraries for certain audio formats, but they're nonfree, so they're not listed build dependencies of the mpd package. Hopefully you know the name of the desired library, but you still have to go search a bit. Having a list from your previous install could be handy - maybe a list of manually installed packages.
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JefromiJun 18 '11 at 14:32